Variant report

Variant	rs3859366
Chromosome Location	chr18:29848436-29848437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29847813..29851392-chr18:29854747..29858581,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11660076	0.96[EUR][1000 genomes]
rs11661174	0.96[EUR][1000 genomes]
rs11661186	0.90[EUR][1000 genomes]
rs11665544	0.96[EUR][1000 genomes]
rs16962918	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962924	0.90[EUR][1000 genomes]
rs16962941	0.96[EUR][1000 genomes]
rs16962953	1.00[ASW][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962965	0.96[EUR][1000 genomes]
rs16962971	1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes]
rs16962974	1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes]
rs16962977	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963184	1.00[CEU][hapmap]
rs28482447	0.96[EUR][1000 genomes]
rs4121653	0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs4462681	1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs60291556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243861	0.90[EUR][1000 genomes]
rs7243963	0.90[EUR][1000 genomes]
rs73419859	1.00[EUR][1000 genomes]
rs8086611	0.96[EUR][1000 genomes]
rs8086990	0.96[EUR][1000 genomes]
rs8087394	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9916917	0.89[EUR][1000 genomes]
rs9947150	0.96[EUR][1000 genomes]
rs9950965	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9953127	0.96[EUR][1000 genomes]
rs9960751	0.96[EUR][1000 genomes]
rs9962307	1.00[GIH][hapmap];0.93[MKK][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29835200-29861600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:29838600-29851400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr18:29838600-29851600	Weak transcription	Stomach Mucosa	stomach
5	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
6	chr18:29843000-29867000	Weak transcription	Brain Angular Gyrus	brain
7	chr18:29844200-29848600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:29845200-29852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr18:29845200-29857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:29845400-29850200	Strong transcription	Adipose Nuclei	Adipose
11	chr18:29845400-29851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr18:29846000-29867000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:29846200-29850400	Weak transcription	Placenta	Placenta
14	chr18:29846200-29850600	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr18:29846400-29851600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:29846600-29851600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr18:29846600-29851600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr18:29846800-29850000	Strong transcription	Fetal Intestine Large	intestine
19	chr18:29846800-29850200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr18:29846800-29850600	Strong transcription	Liver	Liver
21	chr18:29847000-29850000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:29847000-29851400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr18:29847000-29856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:29847400-29850200	Strong transcription	Fetal Lung	lung
25	chr18:29847400-29850400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr18:29847400-29850600	Weak transcription	HSMM	muscle
27	chr18:29847600-29848800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr18:29847600-29849800	Strong transcription	Fetal Kidney	kidney
29	chr18:29847600-29849800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:29847600-29850000	Strong transcription	Brain Substantia Nigra	brain
31	chr18:29847600-29850200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr18:29847600-29850200	Strong transcription	Brain Hippocampus Middle	brain
33	chr18:29847600-29850400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr18:29847600-29850400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:29847600-29850400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr18:29847600-29850400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr18:29847600-29850400	Strong transcription	Fetal Stomach	stomach
38	chr18:29847600-29850400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr18:29847600-29850600	Strong transcription	Gastric	stomach
40	chr18:29847600-29850600	Strong transcription	Pancreas	Pancrea
41	chr18:29847600-29850600	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr18:29847800-29849400	Strong transcription	Right Ventricle	heart
43	chr18:29847800-29849800	Strong transcription	Brain Anterior Caudate	brain
44	chr18:29847800-29850200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:29847800-29850200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:29847800-29850400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr18:29847800-29850600	Strong transcription	Fetal Muscle Leg	muscle
48	chr18:29848000-29848600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:29848000-29848600	Strong transcription	Lung	lung
50	chr18:29848000-29848600	Strong transcription	HepG2	liver

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